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After coming under investigation over an alleged pattern of misconduct while deployed as a staff officer in Afghanistan (long distance phone charges he incurred for personal calls), Shaffer responded by alleging that the U.S. Defense Intelligence Agency (DIA) failed to properly pass on intelligence on 9/11 hijacker Mohamed Atta. Shaffer's allegations subsequently became known as the Able Danger.

In October 2003, according to his later statement to Congress, Shaffer told the 9/11 Commission staff director, Dr. Philip D. Zelikow, that in 2000, a DIA data-mining program known as Able Danger had uncovered two of the three terrorist cells which after 9/11 the FBI determined committed 9/11. Shaffer reportedly told Zelikow that DIA leadership declined to share this information with the FBI because military lawyers expressed concerns about the legality of doing so. Shaffer also asserted that he briefed Director of Central IntelligenceGeorge Tenet on three separate occasions regarding his unit's activities. The 9/11 Commission Report did not mention Shaffer's allegations, but in 2005 and 2006, the Chairman of the House Select Intelligence Committee, Rep. Curt Weldon, publicized Shaffer's allegations in public statements and hearings.[1]

Shaffer alleges, and his Able Danger intelligence colleagues confirm, that the Pentagon repeatedly prevented Able Danger from telling the FBI that they had identified and located Atta, the 9/11 hijackings leader, residing with three other 9/11 hijackers a year before 9/11 in Brooklyn, NYC, and that George Tenet, the FBI director on 9/11 says that if the FBI had been given that information they could have prevented 9/11. Shaffer says, and his Able Danger colleagues confirm, that the Pentagon forbade them on several occasions from communicating the Able Danger investigation results to the FBI, and that as a result nothing was done regarding the Atta cell. [2]

According to US Congressman Weldon, in a speech delivered to Congress, the Pentagon took the following actions against Lt Col. Shaffer as punishment for his repeatedly bringing forward of the above Able Danger facts: Stripped him of his security clearance, put him on indefinite suspension without pay, took away his pension and medical coverage, and had a judge sign a gag order preventing him from telling the press, congress, etc. about Able Danger's discovery of terrorist Mohamed Atta and his cell in NYC. This communication would have, according the CIA Director Tenet, prevented 9/11 hijackings from Boston's Logan International Airport and attacks on the World Trade Center in NYC, the Pentagon in Washington D.C., and other planned targets in the U.S.A. on September 11, 2001. [3]

Shaffer published fictionalized[citation needed] "memoirs" of his time as a reports officer in Afghanistan in book titled Operation Dark Heart. The Defense Department attempted to preserve secrecy of revelations made by the book, by buying up and destroying all 10,000 copies of the book's first, uncensored run, before allowing for the release of a second, censored printing. However, several uncensored pre-release copies were distributed, allowing a person in possession of an earlier copy to compare it to the redacted version to glean what the government considers unfit for public consumption.[4][5]

Shaffer is a frequent guest in the media. He retired from the U.S. Army Reserve. He serves as member of the U.S. Nuclear Strategy Forum.[citation needed] Shaffer was appointed in the summer of 2013 as a Senior Fellow to the London Center for Policy Research.[6]

With William H. Keith, he has written a novel, The Last Line, that was released in hardback in June 2013, and is due out as a paperback in October 2014.[7][8]

In 2012, Shaffer claimed President Obama was "in the White House Situation Room in real-time watching" the attack on the U.S. consulate in Benghazi, Libya, a claim that has been denied by the Obama administration.[9] He further implied the White House was conspiring to prevent charges against released American POW Bowe Bergdahl.[9]